Version 1.7.1
- Added findPeakHeight function to estimate optimal minHeight value based on False Discovery Rate for using in enrichedPeaks
Version 1.5.1
- Fixed bug in enrichedRegions method for RangedDataList objects
VERSION 1.3.1
- Fixed bug in enrichedRegions that caused it to crash when a region had 0 counts in all samples
- Fixed bug in plotMeanCoverage
VERSION 1.1.5
- Added missing documentation
VERSION 1.1.4
- Fixed bug in cmds for method with empty chromosomes
VERSION 1.1.3
- Fixed bug in alignPeaks (no longer directly accessing matchMatrix slot of RangesMatchingList object)
- Added plotMeanCoverage
- Fixed bug in gini for method with no chromosome lengths
VERSION 1.1.2
- Add methods for objects of class GRanges and GRangesList.
- Add set.seed to vignette.
- Use pvec instead of mclapply in tabDuplReads and filterDuplReads.
- Correct rpkm form enrichedRegions and remove it from enrichedPeaks
- Fixed giniCoverage for ranges with low numbers of reads
VERSION 1.1.1
- Adjusted parallel computing in enrichedPeaks so that it no longer spans an uncontrolled number of child processes when mc.cores>1
- Added arguments "labels" and "cex.text" to the plot method for cmdsFit objects.
- Added monotonicity contraint to filterDuplReads and fdrEnrichedCounts to ensure that the estimated FDR decreases with the number of repeats
- Fixed overflow problem in enrichedChrRegions which occurred for long genomes (e.g. human)
- Adjusted behavior of stdPeakLocation so that it is consistent with PeakLocation
- Fixed bug in RPKM calculation by enrichedRegions
- Added option to compute Spearman correlations in cmds
VERSION 0.99
- Adapted enrichedChrRegions to adapt to change in IRanges behavior
- Fixed bug in PeakLocation and stdPeakLocation when strand information was stored in variables of type factor
- Included adjustments for number of reads in each sample for giniCoverage and ssdCoverage
- Improved filterDuplReads, using mixtures of NegBinom
- Adjusted behavior of giniCoverage
- Removed readAlignedBatch, export2Aligned, export2SGR, export2SAM
VERSION 0.2.7
- Fixed bug in filterDuplReads method for 'RangedDataList' which caused it not to pass on arguments to 'RangedData' method
- Changed default value of ppOverAmp=.95 to .99 in filterDuplReads
- Added function rowLogRegLRT
- Fixed bug in alignPeaks caused by change in IRanges behavior.
- Added function coverageDiff to compute difference in coverage between two objects
- Fixed bug regionsCoverage caused by convertion of class "by" objects
- Added plotChrRegions function
- Added enrichedChrRegions function
- Added countHitsWindow function
- stdPeakLocation now allows to set xlim
- plot method for cmdsFit objects now automatically puts both axis on the same scale
- closestGene now allows argument genome to be of class data.frame. This avoids downloading the refflat file at each call.
- Fixed bug in enrichedRegions which caused it to crash when sample1 had more chromosomes than sample2
- Fixed bug in filterDuplReads which caused it to crash when no reads needed to be filtered
- Fixed bug in regionsCoverage which caused it to crash for empty chromosomes
- Removed functions genePlot, rangesPlot (moved to package casper)
- Added regionsCoverage, gridCoverage, stdGrid functions
- Added chipSeqQC function
- enrichedRegions was trying to load multicores library instead of multicore.
- Added ssdCoverage function
- Added enrichedRegions method for RangedDataList objects. This allows comparing proportion of reads in islands across >2 samples.
- Added islandCounts function
- Improved memory usage and speed in filterDuplReads, which no longer relies on countOverlaps from package IRanges
- Changed call to parallel to multicore::parallel to avoid confusion with other packages
VERSION 0.2.5
- Added arguments maxRepeats and ppOverAmp to filterDuplReads to allow it to eliminate reads appearing more than k times (before only k=1 was allowed), or with a large posterior probability of being an artifact
- Added ppEnrichedCounts function
- Modified enrichedRegions to make it compatible with new IRanges version
- Added cmds function to perform MultiDimensional Scaling on sequencing data
- Exact P-value calculation in enrichedRegions is now based on Fisher's exact test, instead of simulations, to increase speed. Changed parameters simulate.p.value and B for exact.
- Chi-square P-value calculation in enrichedRegions is now substantially faster (reduced to about 25% of previous implementation)
- enrichedRegions now selects regions with pval <= pvalFilter, instead of pval < pvalFilter. This allows to obtain all regions by setting pvalFilter=1.
- enrichedRegions now returns reads per kilobase per million (RPKM), as well as raw counts
- Corrected enrichedRegions fold change calculation. Now it is (counts1/nsample1)/(counts2/nsample2) instead of (counts1/(nsample1-counts1))/(counts2/(nsample2-counts2))
- Reduced substantially the amount of memory required by rangesPlot
VERSION 0.2.3
- Fixed issue in enrichedRegions which caused it to return an object with too many spaces
- rangesPlot now produces a warning when no ranges are found in the specified region, but it still produces a plot
- Added genePlot method for signature 'RangedData'
- Fixed issue in genePlot which caused it to ignore the ... argument.
- Fixed issue in genePlot which sometimes caused it to plot additional splicing variants
- Fixed issue in 'filterDuplReads' which caused the returned object to have a too large number of spaces
- Added methods for signature(regions='RangedData', sample1='RangedData', sample2='missing') and
- Fixed bug in enrichedRegions when no hits were found. Also changed argument 'parallelComp' for 'mc.cores', so facilitate using mclapply instead of 'parallel' calls
- Added function tabDuplReads
- Fixed bug in filterDuplReads for RangedData signature which caused it to filter two reads from different chromosomes which had the same start and end positions
- Added extendRanges and filterDuplReads methods for RangedDataList objects. Added mc.cores argument to allow for parallel computing.
- Added export2SGR method for RangedDataList objects.
- export2SGR now uses 'coverage' function instead of 'pileup', as the latter has been deprecated
- Added export2aligned method for RangedDataList objects. Added argument dir.
- alignPeaks now returns an object of the same class as its input, instead of always returning IRangesList objects.
- Added alignPeaks method for RangedDataList objects, and parameter mc.cores to allow parallel computation.
- Major change in readAlignedBatch. Sequences from all files are now returned into a single RangedDataList object. Files are not directly saved to disk as in previous versions.
- Fixed bug in rangesPlot which caused it to plot reads longer than maxFragLength twice
- Fixed bug in genePlot which caused an error for genes with a single exon
- Added PeakLocation function. It produces the same plots as stdPeakLocation except that it doesn't standardize the coordinates.
- Added p-value adjustment in enrichedRegions. Defined methods for the case when sample2 is missing.
- readAlignedBatch now checks for the existence of the files, and returns a warning if they don't.
- Added listOverlap function, which allows to assess the overlap between lists e.g. two ChIP-seq experiments, or ChIP-Seq vs microarray results.
- Corrected bug in alignPeaks which could cause sequences to start at negative indexes.
VERSION 0.2.1
- ReadAlignedBatch now returns 'RangedData' objects. This required substantial structural changes, as new methods had to be defined and many existing ones needed to be adjusted.
- Added methods 'filterDuplReads' and 'mergeRegions' for signature 'RangedData'
- Changed stdPeakLocation to a generic function and defined methods for signatures data.frame and RangedData.
- Added closestGene method for signature 'RangedData'.
- Added enrichedPeaks function to detect peaks in sequencing experiments.
- Added enrichedRegions function to detect significantly enriched regions in sequencing experiments.
- closestGene modified: After bioC upgrade parameter multiple stoped working due to findOverlaps function that deprecated Overlaps function (which was used in previous versions).
- closestGene: Some rbinds have been removed and do.call is used insted to use less memory.
- closestGene: Better control of downloaded refflat files has been added.
- closestGene: new parameter added (promoterInOther). If it's TRUE peaks that are in a promoter region and inside other gene will be assigned to both genes. Only works when multiple=TRUE.
VERSION 0.2.0
- Fixed bug in alignPeaks which caused it not to work when there were some chromosomes with no sequences. Also, now alignPeaks reports the estimated shift.
- readAlignedBatch deletes memory consuming objects after they have been saved to disk. This lowers memory requirements.
- readAlignedBatch forces the chromosome names to start by 'chr', to ensure compatibility with external softwares.
- Added vignette
- Added Rd file for alignPeaks
- Added export2aligned, export2SGR and rangesPlot methods for RangedData and RangedDataList objects.
- export2SGR now longer requires to specify chromosome length for IRangesList and RangedDataList objects. The range of positions where reads have been observed is used instead.
VERSION 0.1.2
- Added vignette
- Exported rangesPlot in NAMESPACE.
- Added function stdPeakLocation to plot peak location in ChIP-Seq and ChIP-chip experiments
- Corrected mismatching arguments in generic definition for genePlot. Also did minor changes to improve label appearance.
- closestGene did not work after upgrading to R 2.10.
VERSION 0.1.1
- closestGene now uses findOverlaps function instead of the deprecated 'overlap'.
- Converted rangesPlot function to S4. Added methods for character, IRanges and IRangesList.
- Converted genePlot function to S4. Added methods for IRanges, IRangesList and CompressedIRangesList objects (additionally to the already existing one for character).
- Added alignPeaks function to align the '+' and '-' reads in ChipSeq experiments
- Now readAlignedBatch returns a RangeDataList object for single end experiments instead of an IRangesList. This allows to store the strand information, which could not be done with the IRangesList object.
- Added export2SAM function
- Added export2aligned method for 'IRanges' objects
- Added 'paired' option in readAlignedBatch
- Changed default type='Bowtie' in readAlignedBatch
- Added genePlot function
- closestGene had an error when looking if a region falls in a promoter.
- Distance to gene added to clsoestGene function.
VERSION 0.1.0
- Added readAlignedBatch function
VERSION 0.0.1
- extendRanges now outputs an IRangesList object instead of a simple list
- Added export2aligned method.
- Added export2SGR method for IRangesList objects
- Added closestGene function.
- Changed "c" for "rbind" in "enrichedRegions.r" line 92 (needed for IRanges version 1.6.0)
- Added require(multicore) to "enrichedRegions.r" and changed mclapply to lapply for non-parallel computation